# DREME 4.12.0
#     command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YAP1/seqs-shuffled
#   positives: 568 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YAP1/seqs-centered (Sat Jan 18 10:32:31 PST 2020)
#   negatives: 568 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--YAP1/seqs-shuffled (Sat Jan 18 10:32:31 PST 2020)
#        host: kali.stanford.edu
#        when: Sat Jan 18 10:47:54 PST 2020

MEME version 4.12.0

ALPHABET "DNA" DNA-LIKE
A "Adenine" CC0000 ~ T "Thymine" 008000
C "Cytosine" 0000CC ~ G "Guanine" FFB300
N "Any base" = ACGT
X = ACGT
. = ACGT
V "Not T" = ACG
H "Not G" = ACT
D "Not C" = AGT
B "Not A" = CGT
M "Amino" = AC
R "Purine" = AG
W "Weak" = AT
S "Strong" = CG
Y "Pyrimidine" = CT
K "Keto" = GT
U = T
END ALPHABET

strands: + -

Background letter frequencies (from dataset):
A 0.314 C 0.187 G 0.187 T 0.312


MOTIF CTWCCA DREME-1

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      CTWCCA     TGGWAG         88         27   8.1e-010   2.6e-005
#           CTTCCA     TGGAAG         55         17   2.1e-006   6.6e-002
#           CTACCA     TGGTAG         34         11   3.2e-004   1.0e+001

letter-probability matrix: alength= 4 w= 6 nsites= 94 E= 2.6e-005
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.372340 0.000000 0.000000 0.627660
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000


MOTIF MAGAAR DREME-2

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      MAGAAR     YTTCTK        264        170   6.2e-009   1.9e-004
#           AAGAAA     TTTCTT        143         90   6.3e-005   2.0e+000
#           AAGAAG     CTTCTT         82         46   4.8e-004   1.5e+001
#           CAGAAG     CTTCTG         46         23   3.0e-003   9.3e+001
#           CAGAAA     TTTCTG         62         37   5.6e-003   1.8e+002

letter-probability matrix: alength= 4 w= 6 nsites= 365 E= 1.9e-004
0.690411 0.309589 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.627397 0.000000 0.372603 0.000000


MOTIF ACGKT DREME-3

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST       ACGKT      AMCGT        158         86   1.2e-007   3.8e-003
#            ACGTT      AACGT         93         47   2.1e-005   6.6e-001
#            ACGGT      ACCGT         78         46   1.5e-003   4.7e+001

letter-probability matrix: alength= 4 w= 5 nsites= 174 E= 3.8e-003
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.459770 0.540230
0.000000 0.000000 0.000000 1.000000


MOTIF GWGATA DREME-4

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      GWGATA     TATCWC         87         34   2.0e-007   5.9e-003
#           GTGATA     TATCAC         41         13   6.1e-005   1.8e+000
#           GAGATA     TATCTC         52         22   2.1e-004   6.3e+000

letter-probability matrix: alength= 4 w= 6 nsites= 95 E= 5.9e-003
0.000000 0.000000 1.000000 0.000000
0.557895 0.000000 0.000000 0.442105
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000


MOTIF GTTMGA DREME-5

#             Word    RC Word        Pos        Neg    P-value    E-value
# BEST      GTTMGA     TCKAAC         85         33   2.4e-007   7.2e-003
#           GTTCGA     TCGAAC         54         19   1.4e-005   4.2e-001
#           GTTAGA     TCTAAC         35         14   1.6e-003   4.6e+001

letter-probability matrix: alength= 4 w= 6 nsites= 90 E= 7.2e-003
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.388889 0.611111 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000


# Stopping reason: E-value threshold exceeded
#    Running time: 21.37 seconds